X-ray Thomson scattering absolute intensity from the f-sum rule in the imaginary-time domain.

We present a formally exact and simulation-free approach for the normalization of X-ray Thomson scattering (XRTS) spectra based on the f-sum rule of the imaginary-time correlation function (ITCF). Our method works for any degree of collectivity, over a broad range of temperatures, and is applicable even in nonequilibrium situations. In addition to giving us model-free access to electronic correlations, this new approach opens up the intriguing possibility to extract a plethora of physical properties from the ITCF based on XRTS experiments.

High-heat flux ball-pen probe head in ASDEX-Upgrade.

A new high heat flux ball-pen probe head installed on the midplane manipulator is currently being used in ASDEX-Upgrade (AUG). The probe was designed to withstand high heat fluxes making possible the investigation of the plasma edge under harsh conditions, such as low power H-mode. Composed of seven pins (four Langmuir probes, mounted in two Mach probe pairs, and three ball-pen probes), the new probe head allows us to measure several plasma parameters simultaneously and with high temporal resolution. A novel method to correct the sheath potential dynamically accounting for the total secondary electron emission is introduced together with applications to obtain the electron temperature and plasma potential profiles. The total secondary electron emission yield is obtained from particle in cell simulations in AUG condition and probe realistic impact angle with respect to the magnetic field. Finally, the probe capability to investigate turbulence around the separatrix of AUG is discussed.

Bridge functions of classical one-component plasmas.

In a recent paper, Lucco Castello et al. [arXiv:2107.03537] performed systematic extractions of classical one-component plasma bridge functions from molecular dynamics simulations and provided an accurate parametrization that was incorporated in their isomorph-based empirically modified hypernetted chain approach for Yukawa one-component plasmas. Here the extraction technique and parametrization strategy are described in detail, while the deficiencies of earlier efforts are discussed. The structural and thermodynamic predictions of the updated version of the integral equation theory approach are compared with extensive available simulation results revealing a truly unprecedented level of accuracy in the entire dense liquid region of the Yukawa phase diagram.

Integral equation theory based dielectric scheme for strongly coupled electron liquids.

In a recent paper, Lucco Castello et al. (arXiv:2107.03537) provided an accurate parameterization of classical one-component plasma bridge functions that was embedded in a novel dielectric scheme for strongly coupled electron liquids. Here, this approach is rigorously formulated, its set of equations is formally derived, and its numerical algorithm is scrutinized. A systematic comparison with available and new path integral Monte Carlo simulations reveals a rather unprecedented agreement especially in terms of the interaction energy and the long wavelength limit of the static local field correction.

Structure and thermodynamics of two-dimensional Yukawa liquids.

The thermodynamic and structural properties of two-dimensional dense Yukawa liquids are studied with molecular dynamics simulations. The "exact" thermodynamic properties are simultaneously employed in an advanced scheme for the determination of an equation of state that shows an unprecedented level of accuracy for the internal energy, pressure, and isothermal compressibility. The "exact" structural properties are utilized to formulate a novel empirical correction to the hypernetted-chain approach that leads to a very high accuracy level in terms of static correlations and thermodynamics.

Testing the isomorph invariance of the bridge functions of Yukawa one-component plasmas.

It has been recently conjectured that bridge functions remain nearly invariant along phase diagram lines of constant excess entropy for the broad class of R-simple liquids. To test this hypothesis, the bridge functions of Yukawa systems are computed outside the correlation void with the Ornstein-Zernike inversion method employing structural input from ultra-accurate molecular dynamics simulations and inside the correlation void with the cavity distribution method employing structural input from ultra-long specially designed molecular dynamics simulations featuring a tagged particle pair. Yukawa bridge functions are revealed to be isomorph invariant to a very high degree. The observed invariance is not exact, however, since isomorphic deviations exceed the overall uncertainties.

Soft mean spherical approximation for dusty plasma liquids: One-component Yukawa systems with plasma shielding.

The structure and thermodynamics of strongly coupled dusty plasmas are investigated with the soft mean spherical approximation. This integral theory approach is analytically solvable for Yukawa pair interactions yielding a closed-form solution for the direct correlation function. The pair correlation function, the structure factor, and basic thermodynamic quantities are calculated for a wide range of parameters. Exact consistency between the "energy"-"virial" thermodynamic routes and approximate consistency between the "energy"-"compressibility" paths is demonstrated. Comparison with extensive molecular dynamics results is carried out and a remarkable agreement from the Coulomb limit to the strongly screened limit is revealed. The soft mean spherical approximation is concluded to be particularly well suited for the study of dusty plasma liquids, uniquely combining simplicity and accuracy.

Spectra of ion density and potential fluctuations in weakly ionized plasmas in the presence of dust grains.

The spectral densities of ion density and electrostatic potential fluctuations are derived in the framework of a self-consistent kinetic model of partially ionized dusty plasmas in the low-frequency regime. Neutral gas density can be responsible for significant modifications of the fluctuation level, hence the inclusion of the effect of neutrals is essential for a more realistic comparison with experiments, especially if spectral measurements are intended for dust diagnostic purposes. Comparison with the multicomponent model, attractive due to its simplicity as compared to the self-consistent one, is carried out to establish its limits of validity. Numerical calculations are performed for parameters typical of low-temperature plasma discharges. A criterion is derived for the omission of plasma discreteness in the low-frequency regime.

Energy metabolism pathways in rat muscle under conditions of simulated microgravity.

Evidence from rats flown in space suggests that there is a decrease in the ability of the soleus muscle to oxidize long chain fatty acids during space flight. The observation suggests that a shift in the pathways involved in muscle fuel utilization in the absence of load on the muscle has occurred. It is also possible that the reduction is part of a general down-sizing of metabolic capacity since energy needs of inactive muscle are necessarily less. The rodent hind limb suspension model has proved to be a useful ground based model for studying the musculo-skeletal systems changes that occur with space flight. Microarray technology permits the screening of a large number of the enzymes of the relevant pathways thereby permitting a distinction to be made between a shift fuel utilization pattern or a general decrease in metabolic activity. The soleus muscle was isolated from 5 control and 5 hindlimb suspended rats (21 days) and the Affymetrix system for assessing gene expression used to determine the impact of hindlimb unloading on fuel pathways within the muscle of each animal. RESULTS: Suspended rats failed to gain weight at the same rate as the controls (337 +/- 5 g vs 318 +/- 6 g, p < 0.05) and muscle mass from the soleus was reduced (135 +/- 3 mg vs 48 +/- 4 mg, p < 0.05). There was a consistent decrease (p < 0.05) in gene expression of proteins involved in fatty acid oxidation in the suspended group whereas glycolytic activity was increased (p < 0.05). Gene expressions of individual key regulatory enzymes reflected these changes. Carnitine palmitoyltransferase I and II were decreased (p < 0.05) whereas expression of hexokinase, phosphofructokinase and pyruvate kinase were increased (p < 0.05). CONCLUSION: Disuse atrophy is associated with a change in mRNA levels of enzymes involved in fuel metabolism indicative of a shift in substrate utilization away from fat towards glucose.

DNA microarray analysis of the contused spinal cord: effect of NMDA receptor inhibition.

Spinal cord injury (SCI)-induced neurodegeneration leads to irreversible and devastating motor and sensory dysfunction. Post-traumatic outcomes are determined by events occurring during the first 24 hours after SCI. An increase in extracellular glutamate concentration to neurotoxic levels is one of the earliest events after SCI. We used Affymetrix DNA oligonucleotide microarrays (with 1,322 DNA probes) analysis to measure gene expression in order to test the hypothesis that SCI-induced N-methyl-D-aspartate (NMDA) receptor activation triggers significant postinjury transcriptional changes. Here we report that SCI, 1 hour after trauma, induced change in mRNA levels of 165 genes and expression sequence tags (ESTs). SCI affected mRNA levels of those genes that regulate predominantly transcription factors, inflammation, cell survival, and membrane excitability. We also report that NMDA receptor inhibition (with -(+)-5-methyl-10,11-dihydro-5H-dibenzo[a,d]-cyclohepten-5,10-imine hydrogen maleate [MK-801]) reversed the effect of SCI on about 50% of the SCI-affected mRNAs. Especially interesting is the finding that NMDA receptor activation participates in the up-regulation of inflammatory factors. Therefore, SCI-induced NMDA receptor activation is one of the dominant, early signals after trauma that leads to changes in mRNA levels of a number of genes relevant to recovery processes. The majority of MK-801 effects on the SCI-induced mRNA changes reported here are novel. Additionally, we found that the MK-801 treatment also changed the mRNA levels of 168 genes and ESTs that had not been affected by SCI alone, and that some of their gene products could have harmful effects on SCI outcome.

Gene expression profiling of acute spinal cord injury reveals spreading inflammatory signals and neuron loss.

We have completed the first large-scale gene expression study of acute spinal cord injury (SCI) in rat. Oligonucleotide microarrays containing 1,200 gene-specific probes were used to quantify mRNA levels, relative to uninjured controls, in spinal cords injured using a standard contusion model. Our results revealed a marked loss of neuron-specific mRNAs at the injury site. The surviving cells showed a characteristic inflammatory response that started at the injury site and spread to the distal cord. Changes in several mRNA levels were associated with putative regenerative responses in the spinal cord. Notably, phosphodiesterase 4, nestin, glia-derived neurite promoting factor, and GAP-43 mRNAs increased significantly. Other mRNAs clustered temporally and spatially with these regeneration-associated genes. Thus we have described global patterns of gene expression following acute SCI, and we have identified targets for future study and possible therapeutic intervention.

Genetic analysis of a La homolog in Drosophila melanogaster.

People afflicted with certain rheumatological auto-immune diseases produce autoantibodies directed against a select group of proteins such as the La auto-antigen. Biochemical studies have revealed La to be a promiscuous RNA-binding protein that appears to play a role in a variety of intracellular activities such as processing and/or transport of RNA polymerase III precursor transcripts and translational regulation from internal ribosome entry sites (IRES). We have previously identified an RNA-binding protein that is a Drosophila melanogaster homolog of La (D-La) and shown that early transcript accumulation throughout the embryo is later refined to be most prevalent in the visceral mesoderm, gut, gonads and salivary glands. Here we report the first in vivo genetic characterization of a La homolog in a multicellular eukaryote. Lethality was observed in homozygous larvae harboring a small chromosomal deletion that removed the D-La gene, which was rescued by an inducible D-La cDNA transgene. This implies that D-La confers essential functions for larval development. In addition, loss of D-La function gives rise to defects in embryonic midgut morphogenesis; one of the midgut defects correlates with loss of Ultrabithorax ( Ubx ) expression along the second midgut constriction. Finally, genetic interactions between chromosomal deficiencies that remove D-La and certain Ubx alleles were demonstrated in adults. Our results support the hypothesis that D-La provides essential functions for proper Drosophila development and imply that the conserved La family of proteins may perform critical developmental functions in higher eukaryotes.

Spire contains actin binding domains and is related to ascidian posterior end mark-5.

Spire is a maternal effect locus that affects both the dorsal-ventral and anterior-posterior axes of the Drosophila egg and embryo. It is required for localization of determinants within the developing oocyte to the posterior pole and to the dorsal anterior corner. During mid-oogenesis, spire mutants display premature microtubule-dependent cytoplasmic streaming, a phenotype that can be mimicked by pharmacological disruption of the actin cytoskeleton with cytochalasin D. Spire has been cloned by transposon tagging and is related to posterior end mark-5, a gene from sea squirts that encodes a posteriorly localized mRNA. Spire mRNA is not, however, localized to the posterior pole. SPIRE also contains two domains with similarity to the actin monomer-binding WH2 domain, and we demonstrate that SPIRE binds to actin in the interaction trap system and in vitro. In addition, SPIRE interacts with the rho family GTPases RHOA, RAC1 and CDC42 in the interaction trap system. Thus, our evidence supports the model that SPIRE links rho family signaling to the actin cytoskeleton.

The Drosophila zygotic lethal gene shuttle craft is required maternally for proper embryonic development.

The Drosophila gene shuttle craft (stc) is expressed zygotically in the embryonic central nervous system (CNS) where it is required to maintain the proper morphology of motoneuronal axon nerve routes following their migration from the ventral cord. Here, we report that a prominent maternal source of STC protein is also present throughout both oogenesis and embryogenesis. To determine whether this maternal component is required in the ovary and/or embryo, we used the Drosophila autosomal dominant female sterile technique to generate germ-line clones that lacked the stc maternal function. Our results demonstrate that a maternally derived source of STC protein is required during embryogenesis but not oogenesis. In contrast to the zygotic phenotype, the primary defect in embryos derived from stc germ-line clones affects segmentation by causing disruptions and deletions in distinct thoracic (T1-T3) and abdominal (A4-A8) segments. These localized defects are responsible for additional phenotypes observed later in development which include gaps in the ventral nerve cord and deletions of denticle belts in the cuticle. An additional phenotype occurring in all other neuromeric segments consists of the misguided migration of motoneuronal axons as they project out of the ventral nerve cord. Thus, the stc zygotic function is required later in development and cannot correct the segmentation and subsequent CNS abnormalities associated with loss of its earlier acting maternally derived activity.

Drosophila clipper/CPSF 30K is a post-transcriptionally regulated nuclear protein that binds RNA containing GC clusters.

An essential component of the mammalian pre-mRNA 3'-end processing machinery is a multimeric protein complex known as cleavage and polyadenylation specificity factor (CPSF). The Drosophila melanogaster gene, clipper ( clp ), encodes a homolog of the CPSF 30K subunit. We have shown previously that CLP possesses N-terminal endoribonucleolytic activity and that the relative expression of its mRNA fluctuates during fly development. In the present study, we report that CLP's C-terminus, containing two CCHC zinc knuckles, confers a binding preference for RNAs that contain G- and/or C-rich clusters. We also show, for the first time, that a member of the highly conserved CPSF 30K family is a nuclear and developmentally regulated protein. Though clp transcripts are detectable throughout embryogenesis, CLP protein is not present. We demonstrate that post-transcriptional regulation of clp mRNA in the embryo occurs by a process that does not involve poly(A) tail length shortening. Thus, a key component of the pre-mRNA 3'-end processing machinery is subject to post-transcriptional regulation during development. These results support the existence of a distinct mechanism controlling eukaryotic gene expression through the regulated processing of pre-mRNAs in the nucleus.

The autosomal chorion locus of the medfly Ceratitis capitata. I. Conserved synteny, amplification and tissue specificity but sequence divergence and altered temporal regulation.

We report the isolation, full sequence characterization, amplification and expression properties of medfly chorion genes corresponding to the autosomal chorion locus of Drosophila. These genes are found adjacent to the paramyosin gene and are organized in the same order and tandem orientation as their Drosophila homologues, although they are spaced further apart. They show substantial sequence divergence from their Drosophila homologues, including novel peptide repeats and a new spacing of the tyrosines, which are known to be cross-linked in Dipteran chorion. The genes are amplified and expressed during oogenesis, as in Drosophila. Three of them are expressed in the same relative temporal order as in Drosophila but the fourth gene, the homologue of s15, shows a clear shift to an earlier expression period. This is the first known instance of changed temporal regulation in dipteran chorion genes.

Cleavage of RNA hairpins mediated by a developmentally regulated CCCH zinc finger protein.

Control of RNA turnover is a major, but poorly understood, aspect of gene regulation. In multicellular organisms, progress toward dissecting RNA turnover pathways has been made by defining some cis-acting sequences that function as either regulatory or cleavage targets (J. G. Belasco and G. Brawerman, Control of Messenger RNA Stability, 1993). However, the identification of genes encoding proteins that regulate or cleave target RNAs has been elusive (C. A. Beelman and R. Parker, Cell 81:79-183, 1995); this gap in knowledge has made it difficult to identify additional components of RNA turnover pathways. We have utilized a modified expression cloning strategy to identify a developmentally regulated gene from Drosophila melanogaster that encodes a RNase that we refer to as Clipper (CLP). Significant sequence matches to open reading frames encoding unknown functions identified from the Caenorhabditis elegans and Saccharomyces cerevisiae genome sequencing projects suggest that all three proteins are members of a new protein family conserved from lower eukaryotes to invertebrates. We demonstrate that a member of this new protein family specifically cleaves RNA hairpins and that this activity resides in a region containing five copies of a previously uncharacterized CCCH zinc finger motif. CLP's endoribonucleolytic activity is distinct from that associated with RNase A (P. Blackburn and S. Moore, p. 317-433, in P. D. Boyer, ed., The Enzymes, vol. XV, part B, 1982) and is unrelated to RNase III processing of rRNAs and tRNAs (J. G. Belasco and G. Brawerman, Control of Messenger RNA Stability, 1993, and S. A. Elela, H. Igel, and M. Ares, Cell 85:115-124, 1995). Our results suggest that CLP may function directly in RNA metabolism.

A homolog of human transcription factor NF-X1 encoded by the Drosophila shuttle craft gene is required in the embryonic central nervous system.

NF-X1 is a novel cytokine-inducible transcription factor that has been implicated in the control of immune responses in humans, presumably by regulating expression of class II major histocompatibility genes. Here we report the cloning and genetic characterization of the first reported NF-X1 homolog, which is encoded by the Drosophila melanogaster shuttle craft (stc) gene. The deduced sequence of the fly and human proteins defines a new family of molecules distinguished by a novel cysteine-rich DNA-binding motif (consisting of seven copies of the consensus sequence Cx3Cx3LxCGx0-5HxCx3CHxGxCx2Cx7-9CxC). We have identified and begun a phenotypic characterization of mutations in the stc gene. stc mutants die at the end of embryogenesis, when they appear to be incapable of coordinating the typical peristaltic contraction waves normally required for embryos to hatch into feeding first instar larvae. Preliminary evidence indicates that the resulting lethality of this behavioral defect is accompanied by subtle morphological abnormalities in the central nervous system, where in wild-type embryos, STC protein is normally localized in the nuclei of repeated cell clusters within each neuromere and brain lobe. Thus, the NF-X1 homolog encoded by the Drosophila stc gene defines a new family of putative transcription factors and plays an essential role in the completion of embryonic development. This study presents the first in vivo genetic analysis of a member of this new protein family.

Developmental characterization of a Drosophila RNA-binding protein homologous to the human systemic lupus erythematosus-associated La/SS-B autoantigen.

Patients with humoral autoimmune diseases such as systemic lupus erythematosus and Sjögren's syndrome contain antibodies in their sera directed against certain normal cellular components such as the La/SS-B autoantigen, an RNA-binding protein believed to function as a putative processor of RNA polymerase III precursor transcripts. We have identified cDNA clones from the fruit fly Drosophila melanogaster that encode a protein displaying significant sequence homology with human La/SS-B. The fly protein (which we refer to as D-La) contains a putative ribonucleoprotein 1 (RNP1) and RNP2 RNA-binding domain. D-La also possesses a leucine zipper motif, suggesting that it may interact with itself or other proteins. Using gel retardation analysis, we show that D-La can bind RNA; in addition, we demonstrate the first reported DNA-binding activity associated with a La protein. Northern (RNA) blot analysis revealed a single 1,600-nucleotide transcript expressed throughout embryonic, larval, pupal, and adult development. Surprisingly, whole-mount in situ hybridization experiments revealed that D-La transcripts are not present in all ovarian tissues. In addition, early expression throughout the embryo is followed by a restricted pattern of mesodermal expression that is later confined to the visceral mesoderm, gonads, gut, and salivary glands. These results suggest that D-La may play a more specialized role during fly development as opposed to a rather general role inferred by its homology to La proteins from other organisms.

Localized maternal and zygotic expression of the gene encoding Drosophila HMG D.

Eukaryotic high mobility group (HMG) proteins such as Drosophila melanogaster HMG D, are thought to be nonhistone components of chromatin. However, we have observed an unusual sequestering of HMG D maternal mRNA within the periphery of oocytes during late oogenesis and zygotic expression confined to the developing embryonic nervous system. Hence, rather than being ubiquitously expressed, HMG D transcripts display a complex pattern of temporal and spatial localization implying a specialized rather than general role during early fly development.